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Bemd#28

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tlfobe wants to merge 17 commits intomastershirtsgroup/terphenyl_simulations:masterfrom bemdshirtsgroup/terphenyl_simulations:bemdCopy head branch name to clipboard

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Commits on Aug 14, 2023

• updating local files from grays-peak, this mainly consists of parameter files and constructed pdb/gro fies using mbuild

  tlfobe

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• merged with master to get some functions from Alpine

  tlfobe

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Commits on Aug 16, 2023

• added directories for pmp tetramer and hexamer REMD simulations with the better ordered atoms. These are giving similar results to what we saw on bridges, but the atom ordering is more consistent b…

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  Theodore Fobe

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• added updated pop tetramer REMD simulations, again these REMD simulations are giving similar results to when I previously ran these on bridges, but theyre updated to run on Alpine and have the bett…

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  Theodore Fobe

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• added pop tetramer and hexamer REMD simulations with updated atom numbering

  

  Theodore Fobe

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• updating some of the analysis scripts signac flow files and labels

  

  Theodore Fobe

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• added the compiled package directory to the gitignore

  

  Theodore Fobe

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• added peptide MD simulation directories, this includes analysis scripts to calculate CVs in unbiased simulations used later for BEMD simulations

  

  Theodore Fobe

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• added BEMD simulations for helical peptide

  

  Theodore Fobe

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• added mom octamer BEMD simulation files

  

  Theodore Fobe

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• added all variants of the terphenyl mop BEMD simulatison Ive made up to this point. This includes simulations with 3 and 4 biased CVs and bespoke simulations for both of those

  

  Theodore Fobe

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Commits on Aug 17, 2023

• added mom terphenyl REMD simulations running with openFF ffs, started a directory with bespoke parameters, but havent run anything it it

  

  Theodore Fobe

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• Merge branch 'bemd' into updating_remd

  

  Theodore Fobe

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• updating some local changes to package scripts

  tlfobe

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• Merge branch 'helical_peptide' of https://github.com/shirtsgroup/terphenyl_simulations into bemd

  tlfobe

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• modified setup.cfg file

  tlfobe

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• Merge branch 'updating_remd' into bemd

  

  Theodore Fobe

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